Difference between revisions of "Sandbox"

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−
* '''Description:''' general stress protein <br/><br/>
+
* '''Description:''' RNase R<br/><br/>
  
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
−
|''dps''
+
|''rnr''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ytkB ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvaJ ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
+
|style="background:#ABCDEF;" align="center"| '''Product''' || exoribonuclease R (EC 3.1.-.-)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || resistance against ethanol stress and survival at low temperatures
+
|style="background:#ABCDEF;" align="center"|'''Function''' || nonspecific degradation of rRNA
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 16 kDa, 4.444  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 88 kDa, 5.703  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 435 bp, 145 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2337 bp, 779 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ytkC]]'', ''[[ytkA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[smpB]]'', ''[[yvaK]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/dps_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/rnr_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/dps_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/rnr_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:dps_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:rnr_context.gif]]
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
|-
 
|-
Line 42: Line 42:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dps.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12584]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14065]
  
 
=== Additional information===
 
=== Additional information===
Line 53: Line 53:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' 3'-5'-exoribonuclease
  
 
* '''Protein family:'''
 
* '''Protein family:'''
Line 81: Line 81:
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU30650]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU33610]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 120: Line 120:
  
 
# H&oumlper et al. (2005)Comprehensive Characterization of the Contribution of Individual ''[[SigB]]''-Dependent General Stress Genes to Stress Resistance of ''Bacillus subtilis''. J. Bact. '''187:''' 2810-2826  [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
 
# H&oumlper et al. (2005)Comprehensive Characterization of the Contribution of Individual ''[[SigB]]''-Dependent General Stress Genes to Stress Resistance of ''Bacillus subtilis''. J. Bact. '''187:''' 2810-2826  [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
 +
# Oussenko, I. A., Abe, T., Ujiie, H., Muto, A. & Bechhofer, D. H. (2005). Participation of 3'-to-5' exoribonucleases in the turnover of ''Bacillus subtilis'' mRNA. J Bacteriol 187:2758-2767. [http://www.ncbi.nlm.nih.gov/sites/entrez/15805522 PubMed]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 16:51, 27 March 2009

  • Description: RNase R

Gene name rnr
Synonyms yvaJ
Essential no
Product exoribonuclease R (EC 3.1.-.-)
Function nonspecific degradation of rRNA
MW, pI 88 kDa, 5.703
Gene length, protein length 2337 bp, 779 aa
Immediate neighbours smpB, yvaK
Gene sequence (+200bp) Protein sequence
Genetic context
Rnr context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: 3'-5'-exoribonuclease
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization:

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: [2]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Regulation:
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

  1. H&oumlper et al. (2005)Comprehensive Characterization of the Contribution of Individual SigB-Dependent General Stress Genes to Stress Resistance of Bacillus subtilis. J. Bact. 187: 2810-2826 PubMed
  2. Oussenko, I. A., Abe, T., Ujiie, H., Muto, A. & Bechhofer, D. H. (2005). Participation of 3'-to-5' exoribonucleases in the turnover of Bacillus subtilis mRNA. J Bacteriol 187:2758-2767. PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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